source: Tutorials/StackingFaults-II/Stacking Faults II.htm @ 2266

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406  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 1"/>
407  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 1"/>
408  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
409  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
410  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
411  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
412  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
413  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
414  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
415  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
416  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
417  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
418  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
419  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
420  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
421  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
422  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
423  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
424  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
425  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
426  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
427  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
428  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
429  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
430  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
431  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
432  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
433  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
434  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
435  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
436  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
437  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
438  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
439  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
440  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
441  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
442  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
443  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
444  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
445  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
446  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
447  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
448  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
449  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
450  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
451  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
452  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
453  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
454  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
455  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
456  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
457  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
458  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
459  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
460  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
461  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
462  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
463  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
464  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
465  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
466  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
467  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
468  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
469  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
470  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
471  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
472  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
473  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
474  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
475  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
476  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
477  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
478  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
479  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
480  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
481  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
482  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
483  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
484  <w:LsdException Locked="false" Priority="19" QFormat="true"
485   Name="Subtle Emphasis"/>
486  <w:LsdException Locked="false" Priority="21" QFormat="true"
487   Name="Intense Emphasis"/>
488  <w:LsdException Locked="false" Priority="31" QFormat="true"
489   Name="Subtle Reference"/>
490  <w:LsdException Locked="false" Priority="32" QFormat="true"
491   Name="Intense Reference"/>
492  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
493  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
494   UnhideWhenUsed="true" Name="Bibliography"/>
495  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
496   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
497  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
498  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
499  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
500  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
501  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
502  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
503  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
504  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
505  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
506  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
507  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
508  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
509  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
510  <w:LsdException Locked="false" Priority="46"
511   Name="Grid Table 1 Light Accent 1"/>
512  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
513  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
514  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
515  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
516  <w:LsdException Locked="false" Priority="51"
517   Name="Grid Table 6 Colorful Accent 1"/>
518  <w:LsdException Locked="false" Priority="52"
519   Name="Grid Table 7 Colorful Accent 1"/>
520  <w:LsdException Locked="false" Priority="46"
521   Name="Grid Table 1 Light Accent 2"/>
522  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
523  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
524  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
525  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
526  <w:LsdException Locked="false" Priority="51"
527   Name="Grid Table 6 Colorful Accent 2"/>
528  <w:LsdException Locked="false" Priority="52"
529   Name="Grid Table 7 Colorful Accent 2"/>
530  <w:LsdException Locked="false" Priority="46"
531   Name="Grid Table 1 Light Accent 3"/>
532  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
533  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
534  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
535  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
536  <w:LsdException Locked="false" Priority="51"
537   Name="Grid Table 6 Colorful Accent 3"/>
538  <w:LsdException Locked="false" Priority="52"
539   Name="Grid Table 7 Colorful Accent 3"/>
540  <w:LsdException Locked="false" Priority="46"
541   Name="Grid Table 1 Light Accent 4"/>
542  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
543  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
544  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
545  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
546  <w:LsdException Locked="false" Priority="51"
547   Name="Grid Table 6 Colorful Accent 4"/>
548  <w:LsdException Locked="false" Priority="52"
549   Name="Grid Table 7 Colorful Accent 4"/>
550  <w:LsdException Locked="false" Priority="46"
551   Name="Grid Table 1 Light Accent 5"/>
552  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
553  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
554  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
555  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
556  <w:LsdException Locked="false" Priority="51"
557   Name="Grid Table 6 Colorful Accent 5"/>
558  <w:LsdException Locked="false" Priority="52"
559   Name="Grid Table 7 Colorful Accent 5"/>
560  <w:LsdException Locked="false" Priority="46"
561   Name="Grid Table 1 Light Accent 6"/>
562  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
563  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
564  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
565  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
566  <w:LsdException Locked="false" Priority="51"
567   Name="Grid Table 6 Colorful Accent 6"/>
568  <w:LsdException Locked="false" Priority="52"
569   Name="Grid Table 7 Colorful Accent 6"/>
570  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
571  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
572  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
573  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
574  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
575  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
576  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
577  <w:LsdException Locked="false" Priority="46"
578   Name="List Table 1 Light Accent 1"/>
579  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
580  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
581  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
582  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
583  <w:LsdException Locked="false" Priority="51"
584   Name="List Table 6 Colorful Accent 1"/>
585  <w:LsdException Locked="false" Priority="52"
586   Name="List Table 7 Colorful Accent 1"/>
587  <w:LsdException Locked="false" Priority="46"
588   Name="List Table 1 Light Accent 2"/>
589  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
590  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
591  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
592  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
593  <w:LsdException Locked="false" Priority="51"
594   Name="List Table 6 Colorful Accent 2"/>
595  <w:LsdException Locked="false" Priority="52"
596   Name="List Table 7 Colorful Accent 2"/>
597  <w:LsdException Locked="false" Priority="46"
598   Name="List Table 1 Light Accent 3"/>
599  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
600  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
601  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
602  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
603  <w:LsdException Locked="false" Priority="51"
604   Name="List Table 6 Colorful Accent 3"/>
605  <w:LsdException Locked="false" Priority="52"
606   Name="List Table 7 Colorful Accent 3"/>
607  <w:LsdException Locked="false" Priority="46"
608   Name="List Table 1 Light Accent 4"/>
609  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
610  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
611  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
612  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
613  <w:LsdException Locked="false" Priority="51"
614   Name="List Table 6 Colorful Accent 4"/>
615  <w:LsdException Locked="false" Priority="52"
616   Name="List Table 7 Colorful Accent 4"/>
617  <w:LsdException Locked="false" Priority="46"
618   Name="List Table 1 Light Accent 5"/>
619  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
620  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
621  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
622  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
623  <w:LsdException Locked="false" Priority="51"
624   Name="List Table 6 Colorful Accent 5"/>
625  <w:LsdException Locked="false" Priority="52"
626   Name="List Table 7 Colorful Accent 5"/>
627  <w:LsdException Locked="false" Priority="46"
628   Name="List Table 1 Light Accent 6"/>
629  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
630  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
631  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
632  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
633  <w:LsdException Locked="false" Priority="51"
634   Name="List Table 6 Colorful Accent 6"/>
635  <w:LsdException Locked="false" Priority="52"
636   Name="List Table 7 Colorful Accent 6"/>
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1089 <o:shapedefaults v:ext="edit" spidmax="1029"/>
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1098
1099<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1100
1101<div class=WordSection1>
1102
1103<h1><span style='mso-fareast-font-family:"Times New Roman"'>Stacking Fault
1104Simulations – II<o:p></o:p></span></h1>
1105
1106<p class=MsoNormal>In this exercise you will simulate some diffraction patterns
1107from kaolinite clays. Kaolinite, <span class=GramE>Al<sub>2</sub>Si<sub>2</sub>O<sub>5</sub>(</span>OH)<sub>4</sub>,
1108is a 1:1 layer silicate with a single unique sheet with AlO<sub>6</sub> <span
1109class=SpellE>octahedra</span> on one side and SiO<sub>4</sub> <span
1110class=SpellE>tetrahedra</span> on the other. The layers stack with an offset to
1111ideally form a triclinic C1 lattice (<span class=SpellE>Bish</span> &amp; Von
1112Dreele, 1989, Clay &amp; Clay Min. 37, 289-296) for a sample of the most
1113ordered form of kaolinite from Keokuk, Iowa. Kaolinites from other locations
1114evidently have stacking faults so that the peaks are displaced, have peculiar
1115shapes and are above a varying background. For the exercise we provide a
1116laboratory Bragg-Brentano pattern of Keokuk kaolinite and a less ordered one
1117from Washington County, Georgia (Clay Minerals Society Standard KGa-1b)
1118collected with <span class=SpellE>CuKa</span> radiation on a Bruker instrument
1119and thus in the Bruker RAW file format. The KGa-1b sample contains a small
1120amount of <span class=SpellE>anatase</span> (TiO<sub>2</sub>) and the Keokuk
1121kaolinite has some <span class=SpellE>dickite</span> (different ordered
1122stacking of kaolinite layers).</p>
1123
1124<p class=MsoNormal>If you have not done so already, start GSAS-II.</p>
1125
1126<h2><span style='mso-fareast-font-family:"Times New Roman"'>Part 1. Creating
1127kaolinite layer<o:p></o:p></span></h2>
1128
1129<p class=MsoNormal>In this initial step we will load from a <span class=SpellE>cif</span>
1130file the structure of kaolinite, draw it to see the layer structure and then
1131transform it into forms suitable for stacking simulations. To begin do <b><span
1132style='font-family:"Calibri",sans-serif'>Import/Phase/from CIF file</span></b>;
1133from the file dialog select <span class=SpellE><b><span style='font-family:
1134"Calibri",sans-serif'>kaolinite.cif</span></b></span>. After the “are you sure”
1135popup, there will be another warning you that 4 atom types (‘O-H’) were not
1136recognized chemical element symbols and they were substituted by <span
1137class=SpellE>Xe</span> to make them obvious in the atom list. Press <b><span
1138style='font-family:"Calibri",sans-serif'>Ok</span></b>; you are offered a
1139chance to change the phase name, I used ‘<b><span style='font-family:"Calibri",sans-serif'>kaolinite</span></b>’.
1140The General tab is displayed (notice the presence of <span class=SpellE>Xe</span>
1141in the element table).</p>
1142
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1168
1169<p class=MsoNormal>To fix the <span class=SpellE>Xe</span> atoms (they should be
1170O), select <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
1171and then double click the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
1172column heading; a small popup will appear. Select <span class=SpellE><b><span
1173style='font-family:"Calibri",sans-serif'>Xe</span></b></span> &amp; press <b><span
1174style='font-family:"Calibri",sans-serif'>Ok</span></b>; the <span class=SpellE>Xe</span>
1175atoms at the bottom of the atom table will be highlighted. Next select <b><span
1176style='font-family:"Calibri",sans-serif'>Edit/Modify atom parameters</span></b>
1177from the Phase Data menu; a new popup will appear.</p>
1178
1179<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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1185
1186<p class=MsoNormal>Select <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
1187&amp; press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>; a
1188periodic table of the element will appear. Select <b><span style='font-family:
1189"Calibri",sans-serif'>O</span></b> from the O-atom pulldown; the structure will
1190be drawn with Al, Si &amp; O atoms only.</p>
1191
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1196</v:shape><![endif]--><![if !vml]><img width=479 height=358
1197src="Stacking%20Faults%20II_files/image006.jpg" v:shapes="Picture_x0020_10"><![endif]></span></p>
1198
1199<p class=MsoNormal>To better visualize the stacking layer, select the <b><span
1200style='font-family:"Calibri",sans-serif'>Draw Atoms</span></b> tab and then double
1201click the empty upper left corner box of the table. All atoms will turn green.
1202Then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Fill unit cell</span></b>;
1203the structure will be redrawn with all atoms that belong in the unit cell.
1204Finally, double click on the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
1205column heading, select <b><span style='font-family:"Calibri",sans-serif'>Al</span></b>
1206&amp; <b><span style='font-family:"Calibri",sans-serif'>Si</span></b> (they
1207will turn green) and then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Fill
1208CN sphere</span></b>. After a bit of rotating the structure around, the
1209layering along the c-axis (blue line) will be evident.</p>
1210
1211<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1212 id="Picture_x0020_11" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:5in;
1213 height:269.25pt;visibility:visible;mso-wrap-style:square'>
1214 <v:imagedata src="Stacking%20Faults%20II_files/image007.jpg" o:title=""/>
1215</v:shape><![endif]--><![if !vml]><img width=480 height=359
1216src="Stacking%20Faults%20II_files/image008.jpg" v:shapes="Picture_x0020_11"><![endif]></span></p>
1217
1218<p class=MsoNormal>One can easily see the layer of SiO<sub>4</sub> <span
1219class=SpellE>tetrahedra</span> and AlO<sub>6</sub> <span class=SpellE>octahedra</span>.
1220Also notice that the next layer (represented by the 4 O atoms at the bottom of
1221the above drawing are offset giving a triclinic lattice.</p>
1222
1223<p class=MsoNormal>The stacking fault simulation calculation via <span
1224class=SpellE>DIFFaX</span> routines requires that the stacking layers be
1225defined in a coordinate system that has the stacking direction perpendicular to
1226the stacking plane defined as the c-axis. This requires transformation of the
1227unit cell and atom coordinates; a suitable tool exists in GSAS-II to do this.
1228Select the <b><span style='font-family:"Calibri",sans-serif'>General</span></b>
1229tab and do <b><span style='font-family:"Calibri",sans-serif'>Compute/Transform</span></b>;
1230a popup window will appear.</p>
1231
1232<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1233 id="Picture_x0020_12" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:262.5pt;
1234 height:254.25pt;visibility:visible;mso-wrap-style:square'>
1235 <v:imagedata src="Stacking%20Faults%20II_files/image009.png" o:title=""/>
1236</v:shape><![endif]--><![if !vml]><img width=350 height=339
1237src="Stacking%20Faults%20II_files/image010.gif" v:shapes="Picture_x0020_12"><![endif]></span></p>
1238
1239<p class=MsoNormal>Note that this allows one to transform the structure
1240according to a matrix and then shift the resultant positions along some vector
1241and then select those that are unique according to a selected space group. The
1242pulldown gives a selection of commonly used transformations; we want the last
1243one, <span class=SpellE><span class=GramE><b><span style='font-family:"Calibri",sans-serif'>abc</span></b></span></span><b><span
1244style='font-family:"Calibri",sans-serif'>*</span></b>, which satisfies the
1245stacking fault requirement. Select it; notice that the space group is changed
1246to P1. Leave this as the kaolinite layer has no symmetry; in other
1247circumstances the layer may have an inversion center in which P-1 should be
1248used. If you press <b><span style='font-family:"Calibri",sans-serif'>Test</span></b>,
1249the new lattice parameters will be shown.</p>
1250
1251<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1252 id="Picture_x0020_13" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:262.5pt;
1253 height:254.25pt;visibility:visible;mso-wrap-style:square'>
1254 <v:imagedata src="Stacking%20Faults%20II_files/image011.png" o:title=""/>
1255</v:shape><![endif]--><![if !vml]><img width=350 height=339
1256src="Stacking%20Faults%20II_files/image012.gif" v:shapes="Picture_x0020_13"><![endif]></span></p>
1257
1258<p class=MsoNormal><span class=GramE>The a</span> &amp; b axes stay the same,
1259but c is now smaller (the interlayer distance in kaolinite) and <span
1260style='font-family:Symbol'>a</span> &amp; <span style='font-family:Symbol'>b</span>
1261= 90 (<span style='font-family:Symbol'>g</span> is unchanged). Press <b><span
1262style='font-family:"Calibri",sans-serif'>Ok</span></b>; a new phase (kaolinite <span
1263class=SpellE><span class=GramE>abc</span></span>*) will be made and its General
1264tab will be shown immediately. Select the <b><span style='font-family:"Calibri",sans-serif'>Draw
1265Atoms</span></b> tab to see the resulting structure.</p>
1266
1267<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1268 id="Picture_x0020_14" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:353.25pt;
1269 height:264pt;visibility:visible;mso-wrap-style:square'>
1270 <v:imagedata src="Stacking%20Faults%20II_files/image013.jpg" o:title=""/>
1271</v:shape><![endif]--><![if !vml]><img width=471 height=352
1272src="Stacking%20Faults%20II_files/image014.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
1273
1274<p class=MsoNormal>To see what this layer looks like with more of it drawn, you
1275can add more unit cells to the drawing; select all the atoms by double clicking
1276the upper left empty box of the Draw atoms table. Do <b style='mso-bidi-font-weight:
1277normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1278minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Add atoms</span></b> and <b
1279style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1280mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>increment</span></b>
1281the 1<sup>st</sup> <b style='mso-bidi-font-weight:normal'><span
1282style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1283mso-hansi-theme-font:minor-latin'>Choose unit cel</span></b>l and press <b
1284style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1285mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>;
1286this will add one unit cell along x. Now select all the atoms again, do <b
1287style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1288mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Add
1289atoms</span></b> and now <b style='mso-bidi-font-weight:normal'><span
1290style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1291mso-hansi-theme-font:minor-latin'>decrement</span></b> the 1<sup>st</sup> <b
1292style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1293mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Choose unit
1294cell</span></b>. Press <b style='mso-bidi-font-weight:normal'><span
1295style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1296mso-hansi-theme-font:minor-latin'>Ok</span></b>; the drawing will now be 3 unit
1297cells wide along x. Repeat this once more <b style='mso-bidi-font-weight:normal'><span
1298style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1299mso-hansi-theme-font:minor-latin'>decrementing</span></b> the 2<sup>nd</sup> <b
1300style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1301mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Choose unit
1302cell</span></b> to give a 3x2 unit cell block of atoms. Double click the <b
1303style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1304mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Style</span></b>
1305column heading and select <b style='mso-bidi-font-weight:normal'><span
1306style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1307mso-hansi-theme-font:minor-latin'>Balls and sticks</span></b>; the drawing
1308should look like (after some zooming/shifting/rotation).</p>
1309
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1347" strokecolor="#ed7d31 [3205]" strokeweight="1.5pt">
1348 <v:stroke dashstyle="longDash" joinstyle="miter"/>
1349 <o:lock v:ext="edit" shapetype="f"/>
1350</v:line><![endif]--><![if !vml]><span style='mso-ignore:vglayout;position:
1351absolute;z-index:251659264;margin-left:12px;margin-top:103px;width:356px;
1352height:202px'><img width=356 height=202
1353src="Stacking%20Faults%20II_files/image015.gif" v:shapes="Straight_x0020_Connector_x0020_16"></span><![endif]><span
1354style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_15"
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1357 <v:imagedata src="Stacking%20Faults%20II_files/image016.jpg" o:title=""/>
1358</v:shape><![endif]--><![if !vml]><img width=477 height=357
1359src="Stacking%20Faults%20II_files/image017.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p>
1360
1361<p class=MsoNormal>I’ll say more about that diagonal line later. This structure
1362is now suitable for use in <span class=SpellE>DIFFaX</span> calculations; the
1363cell has a c-axis that is perpendicular to the ab plane with a length that is
1364the stacking repeat distance. This is a good place to save your project (I
1365called it ‘<b style='mso-bidi-font-weight:normal'><span style='font-family:
1366"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1367minor-latin'>kaolinite’</span></b>).</p>
1368
1369<h2>Part 2. Set up simulation of ideal kaolinite stacking</h2>
1370
1371<p class=MsoNormal>In this part of the tutorial we’ll create a stacking model
1372for Keokuk kaolinite and use <span class=SpellE>DIFFaX</span> to simulate the
1373powder pattern and compare it to some real data. To begin we need a new phase
1374that we can declare as “faulted’. In the main GSAS-II data tree menu do <b
1375style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1376mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data/Add new
1377phase</span></b>; I named it ‘<b style='mso-bidi-font-weight:normal'><span
1378style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1379mso-hansi-theme-font:minor-latin'>Keokuk</span></b>’. The General tab for it
1380will immediately appear.</p>
1381
1382<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1383 id="Picture_x0020_17" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:697.5pt;
1384 height:375pt;visibility:visible;mso-wrap-style:square'>
1385 <v:imagedata src="Stacking%20Faults%20II_files/image018.png" o:title=""/>
1386</v:shape><![endif]--><![if !vml]><img width=930 height=500
1387src="Stacking%20Faults%20II_files/image019.gif" v:shapes="Picture_x0020_17"><![endif]></span></p>
1388
1389<p class=MsoNormal>Change the <b style='mso-bidi-font-weight:normal'><span
1390style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1391mso-hansi-theme-font:minor-latin'>Phase type</span></b> to ‘<b
1392style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1393mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>faulted</span></b>’;
1394the General tab will be redrawn and a new tab <b style='mso-bidi-font-weight:
1395normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1396minor-latin;mso-hansi-theme-font:minor-latin'>‘Layers</span></b>’ will appear.
1397Select it.</p>
1398
1399<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1400 id="Picture_x0020_18" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:612.75pt;
1401 height:363pt;visibility:visible;mso-wrap-style:square'>
1402 <v:imagedata src="Stacking%20Faults%20II_files/image020.png" o:title=""/>
1403</v:shape><![endif]--><![if !vml]><img width=817 height=484
1404src="Stacking%20Faults%20II_files/image021.gif" v:shapes="Picture_x0020_18"><![endif]></span></p>
1405
1406<p class=MsoNormal>We can anticipate (given that kaolinite space group is C1)
1407that the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1408mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Diffraction
1409Laue symmetry</span></b> is <b style='mso-bidi-font-weight:normal'><span
1410style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1411mso-hansi-theme-font:minor-latin'>-1</span></b>. We can enter by hand the
1412lattice parameters from the kaolinite <span class=SpellE><span class=GramE>abc</span></span>*
1413phase but an easier method is available. Do <b style='mso-bidi-font-weight:
1414normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1415minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Copy phase cell</span></b>;
1416a file selection dialog will appear for your current directory and the file <span
1417class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1418"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1419minor-latin'>kaolinite.gpx</span></b></span> should be there. Select it; a
1420small popup will appear listing the available phases. Choose ‘<b
1421style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1422mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>kaolinite <span
1423class=SpellE><span class=GramE>abc</span></span>*</span></b>’ and press <b
1424style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1425mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>;
1426the Layers window will be redrawn with the new lattice parameters.</p>
1427
1428<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1429 id="Picture_x0020_19" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:621.75pt;
1430 height:363pt;visibility:visible;mso-wrap-style:square'>
1431 <v:imagedata src="Stacking%20Faults%20II_files/image022.png" o:title=""/>
1432</v:shape><![endif]--><![if !vml]><img width=829 height=484
1433src="Stacking%20Faults%20II_files/image023.gif" v:shapes="Picture_x0020_19"><![endif]></span></p>
1434
1435<p class=MsoNormal>Next, you need to define the layer. As it would be very tedious
1436to enter 24 atoms by hand, the alternative is to get them from the previously
1437created kaolinite <span class=SpellE><span class=GramE>abc</span></span>*
1438phase. Select the <b style='mso-bidi-font-weight:normal'><span
1439style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1440mso-hansi-theme-font:minor-latin'>Import new layer</span></b> box; the file
1441dialog with <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1442style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1443mso-hansi-theme-font:minor-latin'>kaolinite.gpx</span></b></span> will appear.
1444Select the file and press <b style='mso-bidi-font-weight:normal'><span
1445style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1446mso-hansi-theme-font:minor-latin'>Open</span></b>; again a small popup with two
1447phases listed will appear. Again select <b style='mso-bidi-font-weight:normal'><span
1448style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1449mso-hansi-theme-font:minor-latin'>kaolinite <span class=SpellE><span
1450class=GramE>abc</span></span>*</span></b> and press <b style='mso-bidi-font-weight:
1451normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1452minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>; the Layers page
1453will be redrawn with a layer (named kaolinite) will be filled out.</p>
1454
1455<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1456 id="Picture_x0020_20" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:621.75pt;
1457 height:375pt;visibility:visible;mso-wrap-style:square'>
1458 <v:imagedata src="Stacking%20Faults%20II_files/image024.png" o:title=""/>
1459</v:shape><![endif]--><![if !vml]><img width=829 height=500
1460src="Stacking%20Faults%20II_files/image025.gif" v:shapes="Picture_x0020_20"><![endif]></span></p>
1461
1462<p class=MsoNormal>If you move down to the bottom of the page (if there isn’t a
1463scroll bar, just grab an edge of the window &amp; shift it slightly) to find
1464the one line <b style='mso-bidi-font-weight:normal'><span style='font-family:
1465"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1466minor-latin'>Layer-Layer Transition probabilities</span></b>. Change <span
1467class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1468"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1469minor-latin'>Dz</span></b></span><b style='mso-bidi-font-weight:normal'><span
1470style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1471mso-hansi-theme-font:minor-latin'>=1.0</span></b> and press the plot box; the
1472drawing will show a layer of kaolinite stacked directly above another one.</p>
1473
1474<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1475 id="Picture_x0020_24" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:5in;
1476 height:269.25pt;visibility:visible;mso-wrap-style:square'>
1477 <v:imagedata src="Stacking%20Faults%20II_files/image026.jpg" o:title=""/>
1478</v:shape><![endif]--><![if !vml]><img width=480 height=359
1479src="Stacking%20Faults%20II_files/image027.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>
1480
1481<p class=MsoNormal>Compare that to the stacking in kaolinite.</p>
1482
1483<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1484 id="Picture_x0020_26" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:5in;
1485 height:269.25pt;visibility:visible;mso-wrap-style:square'>
1486 <v:imagedata src="Stacking%20Faults%20II_files/image028.jpg" o:title=""/>
1487</v:shape><![endif]--><![if !vml]><img width=480 height=359
1488src="Stacking%20Faults%20II_files/image029.jpg" v:shapes="Picture_x0020_26"><![endif]></span></p>
1489
1490<p class=MsoNormal>Notice the effect of the offset. The 1<sup>st</sup> row of
1491SiO<sub>4</sub> <span class=SpellE>tetrahedra</span> are positioned directly
1492above the AlO<sub>6</sub> <span class=SpellE>octahedra</span> in the real
1493structure but not in the vertically stacked structure. We can use a bit of
1494simple geometry to work out what the offset is but first let us see what
1495happens in the simulation and how it compares to real data.</p>
1496
1497<h2>Step 3. Import Keokuk kaolinite data and do 1<sup>st</sup> simulation</h2>
1498
1499<p class=MsoNormal>First we need to import the Keokuk kaolinite powder data; do
1500<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1501mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Import/Powder
1502Data/from Bruker RAW file</span></b>. Select <b style='mso-bidi-font-weight:
1503normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1504minor-latin;mso-hansi-theme-font:minor-latin'>Keokuk <span class=SpellE>kaolinite.RAW</span></span></b>
1505from the file dialog box; press <span class=GramE><b style='mso-bidi-font-weight:
1506normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1507minor-latin;mso-hansi-theme-font:minor-latin'>Yes</span></b></span> in the next
1508popup. A new file dialog appears requesting an instrument parameter file; we
1509will use an internal default instead. Press <b style='mso-bidi-font-weight:
1510normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1511minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b> and select <b
1512style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1513mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Defaults for
1514<span class=SpellE>CuKa</span> lab data</span></b> from the next popup. This process
1515will repeat since the RAW file contains two scans. In the next popup, select
1516only <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1517mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>kaolinite <span
1518class=SpellE><span class=GramE>abc</span></span>*</span></b>. There will be two
1519PWDR scans in the GSAS-II data tree; one covers 2<span style='font-family:Symbol'>Q</span>=
152010-90<span style='font-family:"Calibri",sans-serif'>°</span> and the other
1521covers 2<span style='font-family:Symbol'>Q</span>=80-150°. Only the lower part
1522of the first one is going to be used in our simulation work as the calculations
1523become very time consuming for complex structures and high angle data. Select <b
1524style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1525mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR Keokuk <span
1526class=SpellE>kaolinite.RAW</span> Scan 1</span></b> from the GSAS-II data tree
1527make sure it expands; its plot will also show.</p>
1528
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1534src="Stacking%20Faults%20II_files/image031.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>
1535
1536<p class=MsoNormal>Go to <b style='mso-bidi-font-weight:normal'><span
1537style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1538mso-hansi-theme-font:minor-latin'>Limits</span></b> and set <span class=SpellE><b
1539style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1540mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Tmax</span></b></span>
1541to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1542mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>52.0</span></b>;
1543that puts the upper limit in a relatively clear part of the pattern. Then go to
1544Background and set the 1<sup>st</sup> coefficient to 20 (approximately the
1545background at 2Q=18). Next go to <b style='mso-bidi-font-weight:normal'><span
1546style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1547mso-hansi-theme-font:minor-latin'>Sample parameters</span></b> and set the <b
1548style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1549mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
1550scale</span></b> to something reasonable (I chose <b style='mso-bidi-font-weight:
1551normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1552minor-latin;mso-hansi-theme-font:minor-latin'>20.0</span></b>) and make sure
1553the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1554mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Diffractometer
1555type is Bragg-Brentano</span></b>.</p>
1556
1557<p class=MsoNormal>Now we are ready for our 1<sup>st</sup> kaolinite
1558simulation. Go to <b style='mso-bidi-font-weight:normal'><span
1559style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1560mso-hansi-theme-font:minor-latin'>Phases/Keokuk</span></b> and select the <b
1561style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1562mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Layers</span></b>
1563tab. Do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1564mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Simulate
1565pattern</span></b> and press <b style='mso-bidi-font-weight:normal'><span
1566style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1567mso-hansi-theme-font:minor-latin'>Ok</span></b> in the popup. Select the <b
1568style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1569mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Scan 1</span></b>
1570pattern and press <b style='mso-bidi-font-weight:normal'><span
1571style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1572mso-hansi-theme-font:minor-latin'>Ok</span></b>; the simulation will finish
1573quickly (press <b style='mso-bidi-font-weight:normal'><span style='font-family:
1574"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1575minor-latin'>Ok</span></b>) and the new plot will be displayed (I’ve zoomed in
1576a bit).</p>
1577
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1580 height:450pt;visibility:visible;mso-wrap-style:square'>
1581 <v:imagedata src="Stacking%20Faults%20II_files/image032.png" o:title=""/>
1582</v:shape><![endif]--><![if !vml]><img width=700 height=600
1583src="Stacking%20Faults%20II_files/image033.gif" v:shapes="Picture_x0020_29"><![endif]></span>.</p>
1584
1585<p class=MsoNormal>As you can see the simulation (green curve) does not fit the
1586data (blue crosses) at all mostly due to the incorrect layer offset although
1587the 1<sup>st</sup> peak seems to be positioned correctly. To work out the
1588offset consider the drawing of kaolinite.</p>
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1668LA0xMZ5MtNYYb1OYApGdJey24L93POntvczLm+/l29n26kyj7xwbiBcRKOLK1R03BvZvjzcbUD4g
166919g7JgPf5GFbXF7kmNVu4lc670KjpIR9hgbaEIZMa1+1ZNEv3EAst6MbLQaxY6PrEScpt71OouhW
1670W+xYPrQ40ENL1dfuZA28p0d/98HPMX46t/H7p6ksX0pjrq/m8h5UoDn8heEXX9ChEKaDO3HtVW8g
1671WcayJYiIViIkkSyTNaiDgVWarkEXuf6/ofgBAAD//wMAUEsBAi0AFAAGAAgAAAAhALaDOJL+AAAA
16724QEAABMAAAAAAAAAAAAAAAAAAAAAAFtDb250ZW50X1R5cGVzXS54bWxQSwECLQAUAAYACAAAACEA
1673OP0h/9YAAACUAQAACwAAAAAAAAAAAAAAAAAvAQAAX3JlbHMvLnJlbHNQSwECLQAUAAYACAAAACEA
1674ochdx9kBAAD4AwAADgAAAAAAAAAAAAAAAAAuAgAAZHJzL2Uyb0RvYy54bWxQSwECLQAUAAYACAAA
1675ACEANv84Z+AAAAALAQAADwAAAAAAAAAAAAAAAAAzBAAAZHJzL2Rvd25yZXYueG1sUEsFBgAAAAAE
1676AAQA8wAAAEAFAAAAAA==
1677" strokecolor="#ed7d31 [3205]" strokeweight="1.5pt">
1678 <v:stroke joinstyle="miter"/>
1679 <o:lock v:ext="edit" shapetype="f"/>
1680</v:line><![endif]--><![if !vml]><span style='mso-ignore:vglayout;position:
1681absolute;z-index:251660288;margin-left:153px;margin-top:135px;width:3px;
1682height:199px'><img width=3 height=199
1683src="Stacking%20Faults%20II_files/image035.gif" v:shapes="Straight_x0020_Connector_x0020_31"></span><![endif]><span
1684style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_30"
1685 o:spid="_x0000_i1027" type="#_x0000_t75" style='width:360.75pt;height:270pt;
1686 visibility:visible;mso-wrap-style:square'>
1687 <v:imagedata src="Stacking%20Faults%20II_files/image036.jpg" o:title=""/>
1688</v:shape><![endif]--><![if !vml]><img width=481 height=360
1689src="Stacking%20Faults%20II_files/image037.jpg" v:shapes="Picture_x0020_30"><![endif]></span></p>
1690
1691<p class=MsoNormal>The offset <span class=SpellE>Dx</span> is given by the blue
1692arrow in the above drawing of kaolinite and is in fractional coordinates.
1693Geometry gives</p>
1694
1695<p class=MsoNormal><!--[if gte msEquation 12]><m:oMath><i style='mso-bidi-font-style:
1696 normal'><span style='font-family:"Cambria Math",serif'><m:r>Dx</m:r><m:r>= </m:r></span></i><m:f><m:fPr><m:type
1697    m:val="skw"/><span style='font-family:"Cambria Math",serif;mso-ascii-font-family:
1698   "Cambria Math";mso-hansi-font-family:"Cambria Math";font-style:italic;
1699   mso-bidi-font-style:normal'><m:ctrlPr></m:ctrlPr></span></m:fPr><m:num><i
1700   style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif'><m:r>c</m:r></span></i><m:func><m:funcPr><span
1701     style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
1702     mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style:
1703     normal'><m:ctrlPr></m:ctrlPr></span></m:funcPr><m:fName><span
1704     style='font-family:"Cambria Math",serif'><m:r><m:rPr><m:scr m:val="roman"/><m:sty
1705        m:val="p"/></m:rPr>cos</m:r></span></m:fName><m:e><i style='mso-bidi-font-style:
1706     normal'><span style='font-family:"Cambria Math",serif'><m:r>&#946;</m:r></span></i></m:e></m:func></m:num><m:den><i
1707   style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif'><m:r>a</m:r></span></i></m:den></m:f></m:oMath><![endif]--><![if !msEquation]><span
1708style='font-size:12.0pt;font-family:"Times New Roman",serif;mso-fareast-font-family:
1709"Times New Roman";mso-fareast-theme-font:minor-fareast;position:relative;
1710top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language:
1711EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025"
1712 type="#_x0000_t75" style='width:79.5pt;height:19.5pt'>
1713 <v:imagedata src="Stacking%20Faults%20II_files/image038.png" o:title=""
1714  chromakey="white"/>
1715</v:shape><![endif]--><![if !vml]><img width=106 height=26
1716src="Stacking%20Faults%20II_files/image039.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
1717style='mso-spacerun:yes'> </span>Or in this case <b style='mso-bidi-font-weight:
1718normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1719minor-latin;mso-hansi-theme-font:minor-latin'>-0.368</span></b>. Set <span
1720class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1721"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1722minor-latin'>Dx</span></b></span> to this value &amp; repeat simulation.</p>
1723
1724<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1725 id="Picture_x0020_33" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:525pt;
1726 height:450pt;visibility:visible;mso-wrap-style:square'>
1727 <v:imagedata src="Stacking%20Faults%20II_files/image040.png" o:title=""/>
1728</v:shape><![endif]--><![if !vml]><img width=700 height=600
1729src="Stacking%20Faults%20II_files/image041.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
1730
1731<p class=MsoNormal>There is some improvement but some parts are not very well
1732represented. Recall from the triclinic kaolinite lattice parameters that <span
1733style='font-family:Symbol'>a</span> was 91.7°; that will produce a small offset
1734in Dy. Using the same kind of geometry math gives <span class=SpellE><b
1735style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1736mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Dy</span></b></span><b
1737style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1738mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>=-0.0246</span></b>.
1739Enter this value &amp; repeat the simulation again. This gives a much better
1740fit to the observed pattern, but the simulated peaks are too sharp; this can be
1741fixed by changing the U<span class=GramE>,V,W</span> Instrument parameters. I’d
1742just set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1743mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W=40</span></b>
1744and the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1745mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
1746scale</span></b> (in <b style='mso-bidi-font-weight:normal'><span
1747style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1748mso-hansi-theme-font:minor-latin'>Sample parameters</span></b>) to <b
1749style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1750mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>40</span></b>
1751and try again.</p>
1752
1753<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1754 id="Picture_x0020_34" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:525pt;
1755 height:450pt;visibility:visible;mso-wrap-style:square'>
1756 <v:imagedata src="Stacking%20Faults%20II_files/image042.png" o:title=""/>
1757</v:shape><![endif]--><![if !vml]><img width=700 height=600
1758src="Stacking%20Faults%20II_files/image043.gif" v:shapes="Picture_x0020_34"><![endif]></span></p>
1759
1760<p class=MsoNormal>That is a pretty good fit for a stacking simulation. By
1761further hand tweaking of the parameters one can further improve the simulation
1762but based on what we see here we do have the right description of stacking in
1763Keokuk kaolinite. Save your project as you will need it for the next part of
1764the exercise.</p>
1765
1766</div>
1767
1768</body>
1769
1770</html>
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